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SPSens specifications

Information


Unique identifier OMICS_25856
Name SPSens
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Mustafa Khammash

Additional information


https://sourceforge.net/p/spsens/wiki/Home/

Publication for SPSens

SPSens citations

 (4)
library_books

Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits

2016
PLoS Comput Biol
PMCID: 4892630
PMID: 27257684
DOI: 10.1371/journal.pcbi.1004958

[…] Simulations were done using the SPSens software package [] and the ode solver ode45 in MathWorks Matlab 8.1. The derivations of the transfer functions are shown in the Supporting Information. […]

library_books

Accelerated Sensitivity Analysis in High Dimensional Stochastic Reaction Networks

2015
PLoS One
PMCID: 4498611
PMID: 26161544
DOI: 10.1371/journal.pone.0130825

[…] eel [], SensSB [] analyzes parameter sensitivity with deterministic modeling of dynamical systems. Sensitivity analysis for stochastic reaction networks has been implemented in software packages like SPSens [], StochSS [], StochSens [] and ISAP [].In another and complementary direction, recent sensitivity analysis approaches have been proposed as means to quantify the overall behavior of the react […]

library_books

Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains

2014
PLoS Comput Biol
PMCID: 3953644
PMID: 24626049
DOI: 10.1371/journal.pcbi.1003359

[…] etric and exactly rank-one separable, which allows us to use the standard MATLAB solver ode15 s in the sparse format to obtain the univariate factor of a reference solution. In other examples we used SPSens beta 3.4, a massively parallel package for the stochastic simulation of chemical networks (http://sourceforge.net/projects/spsens/) , to construct reference PDFs. The stochastic simulations wer […]

library_books

The Effect of Orthology and Coregulation on Detecting Regulatory Motifs

2010
PLoS One
PMCID: 2815771
PMID: 20140085
DOI: 10.1371/journal.pone.0008938

[…] he algorithms not being able to detect the motif sites in the distant orthologs. This was confirmed by specifically calculating the sensitivity in the distant ortholog (species-dependent sensitivity, spSens) which was indeed lower than the overall sensitivity (results in ). In this example where the synthetic datasets were particularly easy to prealign (equal sequence lengths), including the dista […]

Citations

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SPSens institution(s)
Department of Biosystems Science and Engineering, ETH–Zurich, Basel, Switzerland; Department of Mathematics and Statistics, University of Maryland, Baltimore County, Baltimore, MD, USA
SPSens funding source(s)
Supported by the National Science Foundation through Grant ECCS-0835847 and by the Human Frontier Science Program Grant RGP0061/2011.

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